9WSC | pdb_00009wsc

Crystal structure of PcNLP485 effector protein from P.capsici

PDB DOI: https://doi.org/10.2210/pdb9WSC/pdb

Classification: TOXIN
Organism(s): Phytophthora capsici
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-09-12 Released: 2025-10-15
Deposition Author(s): Zhao, W.L., Zhang, X.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.204 (Depositor), 0.204 (DCC)
R-Value Work:
0.171 (Depositor), 0.172 (DCC)
R-Value Observed:
0.172 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of PcNLP485 effector protein from P.capsici

Zhao, W.L., Zhang, X.G.

To be published.

Macromolecule Content

Total Structure Weight: 26.06 kDa
Atom Count: 2,114
Modeled Residue Count: 222
Deposited Residue Count: 232
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NLP effector protein Pc129485	A	232	Phytophthora capsici	Mutation(s): 0 Gene Names: Pc129485
UniProt
Find proteins for A0A2R2Z574 (Phytophthora capsici) Explore A0A2R2Z574 Go to UniProtKB: A0A2R2Z574
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A2R2Z574
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.204 (Depositor), 0.204 (DCC)
R-Value Work: 0.171 (Depositor), 0.172 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.764	α = 90
b = 63.366	β = 90
c = 79.035	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SOLVE	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	CARS-25-03B

Revision History (Full details and data files)

Version 1.0: 2025-10-15
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.